Fig. 6

Gene expression changes broadly correspond with LAD states across developmental trajectories. A Fold change in gene expression of differentiated cell types relative to ESCs for each LAD category. Change indicated by arrows in the panel on the right. Points are mean and gray ribbons indicate standard deviation. ANOVA test is significant for all cell types. B LAD assignments and expression levels of characteristic genes for each cell type show that many canonically expressed genes are nonLADs in their respective cell types and located within LADs in alternative cell types. C Gene LAD assignment changes across cells from the mesoderm lineage. T1-LADs in dark purple, T2-LADs in light purple, nonLADs in gray. Genes rarely move from T1-LADs to nonLADs or vice versa, with T2-LADs showing the greatest gene occupancy gains and losses. D,E Track views of LB1 and LAD calls surrounding TBX20 and SCCPDH and the SCCPDH enhancer show gene LAD occupancy changes (TBX20) and enhancer-LAD occupancy changes (SCCPDH enhancer) along a cell trajectory in the mesoderm lineage (ESCs to mesoderm progenitors to cardiac myocytes)